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- PDB-7cr8: Synechocystis Cas1-Cas2-prespacerL complex -

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基本情報

登録情報
データベース: PDB / ID: 7cr8
タイトルSynechocystis Cas1-Cas2-prespacerL complex
要素
  • (DNA (36-MER)) x 2
  • CRISPR-associated endonuclease Cas1
  • CRISPR-associated endoribonuclease Cas2 1
キーワードIMMUNE SYSTEM/DNA (免疫系) / CRISPR (CRISPR) / adaptation (適応 (生物学)) / IMMUNE SYSTEM-DNA complex (免疫系)
機能・相同性
機能・相同性情報


maintenance of CRISPR repeat elements / RNA endonuclease activity / DNA endonuclease activity / defense response to virus / 加水分解酵素; エステル加水分解酵素 / DNA binding / metal ion binding
類似検索 - 分子機能
CRISPR-associated protein Cas1, cyanobacteria-type / CRISPR-associated endonuclease Cas2 / Virulence-associated protein D / CRISPR associated protein Cas2 / CRISPR associated protein Cas2 / CRISPR-associated endonuclease Cas1, N-terminal domain / CRISPR-associated protein Cas1 / CRISPR-associated endonuclease Cas1, C-terminal domain / CRISPR associated protein Cas1
類似検索 - ドメイン・相同性
デオキシリボ核酸 / DNA (> 10) / CRISPR-associated endoribonuclease Cas2 1 / CRISPR-associated endonuclease Cas1
類似検索 - 構成要素
生物種Synechocystis sp. (バクテリア)
synthetic construct (人工物)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 3.7 Å
データ登録者Yu, Y. / Chen, Q.
引用ジャーナル: Nucleic Acids Res / 年: 2021
タイトル: Mechanisms of spacer acquisition by sequential assembly of the adaptation module in Synechocystis.
著者: Chengyong Wu / Dongmei Tang / Jie Cheng / Daojun Hu / Zejing Yang / Xue Ma / Haihuai He / Shaohua Yao / Tian-Min Fu / Yamei Yu / Qiang Chen /
要旨: CRISPR-Cas immune systems process and integrate short fragments of DNA from new invaders as spacers into the host CRISPR locus to establish molecular memory of prior infection, which is also known as ...CRISPR-Cas immune systems process and integrate short fragments of DNA from new invaders as spacers into the host CRISPR locus to establish molecular memory of prior infection, which is also known as adaptation in the field. Some CRISPR-Cas systems rely on Cas1 and Cas2 to complete the adaptation process, which has been characterized in a few systems. In contrast, many other CRISPR-Cas systems require an additional factor of Cas4 for efficient adaptation, the mechanism of which remains less understood. Here we present biochemical reconstitution of the Synechocystis sp. PCC6803 type I-D adaptation system, X-ray crystal structures of Cas1-Cas2-prespacer complexes, and negative stained electron microscopy structure of the Cas4-Cas1 complex. Cas4 and Cas2 compete with each other to interact with Cas1. In the absence of prespacer, Cas4 but not Cas2 assembles with Cas1 into a very stable complex for processing the prespacer. Strikingly, the Cas1-prespacer complex develops a higher binding affinity toward Cas2 to form the Cas1-Cas2-prespacer ternary complex for integration. Together, we show a two-step sequential assembly mechanism for the type I-D adaptation module of Synechocystis, in which Cas4-Cas1 and Cas1-Cas2 function as two exclusive complexes for prespacer processing, capture, and integration.
履歴
登録2020年8月12日登録サイト: PDBJ / 処理サイト: PDBJ
改定 1.02021年3月31日Provider: repository / タイプ: Initial release
改定 1.12023年11月29日Group: Data collection / Database references / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

ダウンロードとリンク

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集合体

登録構造単位
I: CRISPR-associated endonuclease Cas1
J: CRISPR-associated endonuclease Cas1
K: CRISPR-associated endonuclease Cas1
L: CRISPR-associated endonuclease Cas1
M: CRISPR-associated endoribonuclease Cas2 1
N: CRISPR-associated endoribonuclease Cas2 1
O: DNA (36-MER)
P: DNA (36-MER)
Q: CRISPR-associated endonuclease Cas1
R: CRISPR-associated endonuclease Cas1
S: CRISPR-associated endonuclease Cas1
T: CRISPR-associated endonuclease Cas1
U: CRISPR-associated endoribonuclease Cas2 1
V: CRISPR-associated endoribonuclease Cas2 1
W: DNA (36-MER)
X: DNA (36-MER)
a: CRISPR-associated endonuclease Cas1
b: CRISPR-associated endonuclease Cas1
c: CRISPR-associated endonuclease Cas1
d: CRISPR-associated endonuclease Cas1
e: CRISPR-associated endoribonuclease Cas2 1
f: CRISPR-associated endoribonuclease Cas2 1
g: DNA (36-MER)
h: DNA (36-MER)
i: CRISPR-associated endonuclease Cas1
j: CRISPR-associated endonuclease Cas1
k: CRISPR-associated endonuclease Cas1
l: CRISPR-associated endonuclease Cas1
m: CRISPR-associated endoribonuclease Cas2 1
n: CRISPR-associated endoribonuclease Cas2 1
o: DNA (36-MER)
p: DNA (36-MER)
q: CRISPR-associated endonuclease Cas1
r: CRISPR-associated endonuclease Cas1
s: CRISPR-associated endonuclease Cas1
t: CRISPR-associated endonuclease Cas1
u: CRISPR-associated endoribonuclease Cas2 1
v: CRISPR-associated endoribonuclease Cas2 1
w: DNA (36-MER)
x: DNA (36-MER)
A: CRISPR-associated endonuclease Cas1
B: CRISPR-associated endonuclease Cas1
C: CRISPR-associated endonuclease Cas1
D: CRISPR-associated endonuclease Cas1
E: CRISPR-associated endoribonuclease Cas2 1
F: CRISPR-associated endoribonuclease Cas2 1
G: DNA (36-MER)
H: DNA (36-MER)


分子量 (理論値)分子数
合計 (水以外)1,179,72048
ポリマ－1,179,72048
非ポリマー00
水0
1
I: CRISPR-associated endonuclease Cas1
J: CRISPR-associated endonuclease Cas1
K: CRISPR-associated endonuclease Cas1
L: CRISPR-associated endonuclease Cas1
M: CRISPR-associated endoribonuclease Cas2 1
N: CRISPR-associated endoribonuclease Cas2 1
O: DNA (36-MER)
P: DNA (36-MER)


分子量 (理論値)分子数
合計 (水以外)196,6208
ポリマ－196,6208
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area21710 Å2
ΔGint-113 kcal/mol
Surface area76110 Å2
手法PISA
2
Q: CRISPR-associated endonuclease Cas1
R: CRISPR-associated endonuclease Cas1
S: CRISPR-associated endonuclease Cas1
T: CRISPR-associated endonuclease Cas1
U: CRISPR-associated endoribonuclease Cas2 1
V: CRISPR-associated endoribonuclease Cas2 1
W: DNA (36-MER)
X: DNA (36-MER)


分子量 (理論値)分子数
合計 (水以外)196,6208
ポリマ－196,6208
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area21730 Å2
ΔGint-115 kcal/mol
Surface area76090 Å2
手法PISA
3
a: CRISPR-associated endonuclease Cas1
b: CRISPR-associated endonuclease Cas1
c: CRISPR-associated endonuclease Cas1
d: CRISPR-associated endonuclease Cas1
e: CRISPR-associated endoribonuclease Cas2 1
f: CRISPR-associated endoribonuclease Cas2 1
g: DNA (36-MER)
h: DNA (36-MER)


分子量 (理論値)分子数
合計 (水以外)196,6208
ポリマ－196,6208
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area21690 Å2
ΔGint-113 kcal/mol
Surface area76250 Å2
手法PISA
4
i: CRISPR-associated endonuclease Cas1
j: CRISPR-associated endonuclease Cas1
k: CRISPR-associated endonuclease Cas1
l: CRISPR-associated endonuclease Cas1
m: CRISPR-associated endoribonuclease Cas2 1
n: CRISPR-associated endoribonuclease Cas2 1
o: DNA (36-MER)
p: DNA (36-MER)


分子量 (理論値)分子数
合計 (水以外)196,6208
ポリマ－196,6208
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area21590 Å2
ΔGint-111 kcal/mol
Surface area76520 Å2
手法PISA
5
q: CRISPR-associated endonuclease Cas1
r: CRISPR-associated endonuclease Cas1
s: CRISPR-associated endonuclease Cas1
t: CRISPR-associated endonuclease Cas1
u: CRISPR-associated endoribonuclease Cas2 1
v: CRISPR-associated endoribonuclease Cas2 1
w: DNA (36-MER)
x: DNA (36-MER)


分子量 (理論値)分子数
合計 (水以外)196,6208
ポリマ－196,6208
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area21770 Å2
ΔGint-119 kcal/mol
Surface area76260 Å2
手法PISA
6
A: CRISPR-associated endonuclease Cas1
B: CRISPR-associated endonuclease Cas1
C: CRISPR-associated endonuclease Cas1
D: CRISPR-associated endonuclease Cas1
E: CRISPR-associated endoribonuclease Cas2 1
F: CRISPR-associated endoribonuclease Cas2 1
G: DNA (36-MER)
H: DNA (36-MER)


分子量 (理論値)分子数
合計 (水以外)196,6208
ポリマ－196,6208
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area21730 Å2
ΔGint-111 kcal/mol
Surface area76210 Å2
手法PISA
単位格子
Length a, b, c (Å)185.401, 185.401, 382.849
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31
Space group name HallP31
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID
11
21
31
41
51
61
71
81
91
101
111
121
131
141
151
161
171
181
191
201
211
221
231
241
12
22
32
42
52
62
72
82
92
102
112
122
13
23
33
43
53
63
14
24
34
44
54
64

NCSドメイン領域:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111SERSERLYSLYS(chain 'A' and (resid 2 through 26 or resid 30...AOA2 - 2513 - 36
121SERSERGLNGLN(chain 'A' and (resid 2 through 26 or resid 30...AOA30 - 12841 - 139
131PROPROPHEPHE(chain 'A' and (resid 2 through 26 or resid 30...AOA132 - 258143 - 269
141PHEPHELYSLYS(chain 'A' and (resid 2 through 26 or resid 30...AOA265 - 288276 - 299
151PHEPHEVALVAL(chain 'A' and (resid 2 through 26 or resid 30...AOA292 - 323303 - 334
261SERSERLYSLYS(chain 'B' and (resid 2 through 26 or resid 30...BPA2 - 2513 - 36
271SERSERGLNGLN(chain 'B' and (resid 2 through 26 or resid 30...BPA30 - 12841 - 139
281PROPROPHEPHE(chain 'B' and (resid 2 through 26 or resid 30...BPA132 - 258143 - 269
291PHEPHELYSLYS(chain 'B' and (resid 2 through 26 or resid 30...BPA265 - 288276 - 299
2101PHEPHEVALVAL(chain 'B' and (resid 2 through 26 or resid 30...BPA292 - 323303 - 334
3111SERSERLYSLYS(chain 'C' and (resid 2 through 26 or resid 30...CQA2 - 2513 - 36
3121SERSERGLNGLN(chain 'C' and (resid 2 through 26 or resid 30...CQA30 - 12841 - 139
3131PROPROPHEPHE(chain 'C' and (resid 2 through 26 or resid 30...CQA132 - 258143 - 269
3141PHEPHELYSLYS(chain 'C' and (resid 2 through 26 or resid 30...CQA265 - 288276 - 299
3151PHEPHEVALVAL(chain 'C' and (resid 2 through 26 or resid 30...CQA292 - 323303 - 334
4161SERSERLYSLYS(chain 'D' and (resid 2 through 26 or resid 30...DRA2 - 2513 - 36
4171SERSERGLNGLN(chain 'D' and (resid 2 through 26 or resid 30...DRA30 - 12841 - 139
4181PROPROPHEPHE(chain 'D' and (resid 2 through 26 or resid 30...DRA132 - 258143 - 269
4191PHEPHELYSLYS(chain 'D' and (resid 2 through 26 or resid 30...DRA265 - 288276 - 299
4201PHEPHEVALVAL(chain 'D' and (resid 2 through 26 or resid 30...DRA292 - 323303 - 334
5211SERSERLYSLYS(chain 'I' and (resid 2 through 26 or resid 30...IA2 - 2513 - 36
5221SERSERGLNGLN(chain 'I' and (resid 2 through 26 or resid 30...IA30 - 12841 - 139
5231PROPROPHEPHE(chain 'I' and (resid 2 through 26 or resid 30...IA132 - 258143 - 269
5241PHEPHELYSLYS(chain 'I' and (resid 2 through 26 or resid 30...IA265 - 288276 - 299
5251PHEPHEVALVAL(chain 'I' and (resid 2 through 26 or resid 30...IA292 - 323303 - 334
6261SERSERLYSLYS(chain 'J' and (resid 2 through 26 or resid 30...JB2 - 2513 - 36
6271SERSERGLNGLN(chain 'J' and (resid 2 through 26 or resid 30...JB30 - 12841 - 139
6281PROPROPHEPHE(chain 'J' and (resid 2 through 26 or resid 30...JB132 - 258143 - 269
6291PHEPHELYSLYS(chain 'J' and (resid 2 through 26 or resid 30...JB265 - 288276 - 299
6301PHEPHEVALVAL(chain 'J' and (resid 2 through 26 or resid 30...JB292 - 323303 - 334
7311SERSERLYSLYS(chain 'K' and (resid 2 through 26 or resid 30...KC2 - 2513 - 36
7321SERSERGLNGLN(chain 'K' and (resid 2 through 26 or resid 30...KC30 - 12841 - 139
7331PROPROPHEPHE(chain 'K' and (resid 2 through 26 or resid 30...KC132 - 258143 - 269
7341PHEPHELYSLYS(chain 'K' and (resid 2 through 26 or resid 30...KC265 - 288276 - 299
7351PHEPHEVALVAL(chain 'K' and (resid 2 through 26 or resid 30...KC292 - 323303 - 334
8361SERSERLYSLYS(chain 'L' and (resid 2 through 26 or resid 30...LD2 - 2513 - 36
8371SERSERGLNGLN(chain 'L' and (resid 2 through 26 or resid 30...LD30 - 12841 - 139
8381PROPROPHEPHE(chain 'L' and (resid 2 through 26 or resid 30...LD132 - 258143 - 269
8391PHEPHELYSLYS(chain 'L' and (resid 2 through 26 or resid 30...LD265 - 288276 - 299
8401PHEPHEVALVAL(chain 'L' and (resid 2 through 26 or resid 30...LD292 - 323303 - 334
9411SERSERLYSLYS(chain 'Q' and (resid 2 through 26 or resid 30...QI2 - 2513 - 36
9421SERSERGLNGLN(chain 'Q' and (resid 2 through 26 or resid 30...QI30 - 12841 - 139
9431PROPROPHEPHE(chain 'Q' and (resid 2 through 26 or resid 30...QI132 - 258143 - 269
9441PHEPHELYSLYS(chain 'Q' and (resid 2 through 26 or resid 30...QI265 - 288276 - 299
9451PHEPHEVALVAL(chain 'Q' and (resid 2 through 26 or resid 30...QI292 - 323303 - 334
10461SERSERLYSLYS(chain 'R' and (resid 2 through 26 or resid 30...RJ2 - 2513 - 36
10471SERSERGLNGLN(chain 'R' and (resid 2 through 26 or resid 30...RJ30 - 12841 - 139
10481PROPROPHEPHE(chain 'R' and (resid 2 through 26 or resid 30...RJ132 - 258143 - 269
10491PHEPHELYSLYS(chain 'R' and (resid 2 through 26 or resid 30...RJ265 - 288276 - 299
10501PHEPHEVALVAL(chain 'R' and (resid 2 through 26 or resid 30...RJ292 - 323303 - 334
11511SERSERLYSLYS(chain 'S' and (resid 2 through 26 or resid 30...SK2 - 2513 - 36
11521SERSERGLNGLN(chain 'S' and (resid 2 through 26 or resid 30...SK30 - 12841 - 139
11531PROPROPHEPHE(chain 'S' and (resid 2 through 26 or resid 30...SK132 - 258143 - 269
11541PHEPHELYSLYS(chain 'S' and (resid 2 through 26 or resid 30...SK265 - 288276 - 299
11551PHEPHEVALVAL(chain 'S' and (resid 2 through 26 or resid 30...SK292 - 323303 - 334
12561SERSERLYSLYS(chain 'T' and (resid 2 through 26 or resid 30...TL2 - 2513 - 36
12571SERSERGLNGLN(chain 'T' and (resid 2 through 26 or resid 30...TL30 - 12841 - 139
12581PROPROPHEPHE(chain 'T' and (resid 2 through 26 or resid 30...TL132 - 258143 - 269
12591PHEPHELYSLYS(chain 'T' and (resid 2 through 26 or resid 30...TL265 - 288276 - 299
12601PHEPHEVALVAL(chain 'T' and (resid 2 through 26 or resid 30...TL292 - 323303 - 334
13611SERSERLYSLYS(chain 'a' and (resid 2 through 26 or resid 30...aQ2 - 2513 - 36
13621SERSERGLNGLN(chain 'a' and (resid 2 through 26 or resid 30...aQ30 - 12841 - 139
13631PROPROPHEPHE(chain 'a' and (resid 2 through 26 or resid 30...aQ132 - 258143 - 269
13641PHEPHELYSLYS(chain 'a' and (resid 2 through 26 or resid 30...aQ265 - 288276 - 299
13651PHEPHEVALVAL(chain 'a' and (resid 2 through 26 or resid 30...aQ292 - 323303 - 334
14661SERSERLYSLYS(chain 'b' and (resid 2 through 26 or resid 30...bR2 - 2513 - 36
14671SERSERGLNGLN(chain 'b' and (resid 2 through 26 or resid 30...bR30 - 12841 - 139
14681PROPROPHEPHE(chain 'b' and (resid 2 through 26 or resid 30...bR132 - 258143 - 269
14691PHEPHELYSLYS(chain 'b' and (resid 2 through 26 or resid 30...bR265 - 288276 - 299
14701PHEPHEVALVAL(chain 'b' and (resid 2 through 26 or resid 30...bR292 - 323303 - 334
15711SERSERLYSLYS(chain 'c' and (resid 2 through 26 or resid 30...cS2 - 2513 - 36
15721SERSERGLNGLN(chain 'c' and (resid 2 through 26 or resid 30...cS30 - 12841 - 139
15731PROPROPHEPHE(chain 'c' and (resid 2 through 26 or resid 30...cS132 - 258143 - 269
15741PHEPHELYSLYS(chain 'c' and (resid 2 through 26 or resid 30...cS265 - 288276 - 299
15751PHEPHEVALVAL(chain 'c' and (resid 2 through 26 or resid 30...cS292 - 323303 - 334
16761SERSERLYSLYS(chain 'd' and (resid 2 through 26 or resid 30...dT2 - 2513 - 36
16771SERSERGLNGLN(chain 'd' and (resid 2 through 26 or resid 30...dT30 - 12841 - 139
16781PROPROPHEPHE(chain 'd' and (resid 2 through 26 or resid 30...dT132 - 258143 - 269
16791PHEPHELYSLYS(chain 'd' and (resid 2 through 26 or resid 30...dT265 - 288276 - 299
16801PHEPHEVALVAL(chain 'd' and (resid 2 through 26 or resid 30...dT292 - 323303 - 334
17811SERSERLYSLYS(chain 'i' and (resid 2 through 26 or resid 30...iY2 - 2513 - 36
17821SERSERGLNGLN(chain 'i' and (resid 2 through 26 or resid 30...iY30 - 12841 - 139
17831PROPROPHEPHE(chain 'i' and (resid 2 through 26 or resid 30...iY132 - 258143 - 269
17841PHEPHELYSLYS(chain 'i' and (resid 2 through 26 or resid 30...iY265 - 288276 - 299
17851PHEPHEVALVAL(chain 'i' and (resid 2 through 26 or resid 30...iY292 - 323303 - 334
18861SERSERLYSLYS(chain 'j' and (resid 2 through 26 or resid 30...jZ2 - 2513 - 36
18871SERSERGLNGLN(chain 'j' and (resid 2 through 26 or resid 30...jZ30 - 12841 - 139
18881PROPROPHEPHE(chain 'j' and (resid 2 through 26 or resid 30...jZ132 - 258143 - 269
18891PHEPHELYSLYS(chain 'j' and (resid 2 through 26 or resid 30...jZ265 - 288276 - 299
18901PHEPHEVALVAL(chain 'j' and (resid 2 through 26 or resid 30...jZ292 - 323303 - 334
19911SERSERLYSLYS(chain 'k' and (resid 2 through 26 or resid 30...kAA2 - 2513 - 36
19921SERSERGLNGLN(chain 'k' and (resid 2 through 26 or resid 30...kAA30 - 12841 - 139
19931PROPROPHEPHE(chain 'k' and (resid 2 through 26 or resid 30...kAA132 - 258143 - 269
19941PHEPHELYSLYS(chain 'k' and (resid 2 through 26 or resid 30...kAA265 - 288276 - 299
19951PHEPHEVALVAL(chain 'k' and (resid 2 through 26 or resid 30...kAA292 - 323303 - 334
20961SERSERLYSLYS(chain 'l' and (resid 2 through 26 or resid 30...lBA2 - 2513 - 36
20971SERSERGLNGLN(chain 'l' and (resid 2 through 26 or resid 30...lBA30 - 12841 - 139
20981PROPROPHEPHE(chain 'l' and (resid 2 through 26 or resid 30...lBA132 - 258143 - 269
20991PHEPHELYSLYS(chain 'l' and (resid 2 through 26 or resid 30...lBA265 - 288276 - 299
201001PHEPHEVALVAL(chain 'l' and (resid 2 through 26 or resid 30...lBA292 - 323303 - 334
211011SERSERLYSLYS(chain 'q' and (resid 2 through 26 or resid 30...qGA2 - 2513 - 36
211021SERSERGLNGLN(chain 'q' and (resid 2 through 26 or resid 30...qGA30 - 12841 - 139
211031PROPROPHEPHE(chain 'q' and (resid 2 through 26 or resid 30...qGA132 - 258143 - 269
211041PHEPHELYSLYS(chain 'q' and (resid 2 through 26 or resid 30...qGA265 - 288276 - 299
211051PHEPHEVALVAL(chain 'q' and (resid 2 through 26 or resid 30...qGA292 - 323303 - 334
221061SERSERLYSLYS(chain 'r' and (resid 2 through 26 or resid 30...rHA2 - 2513 - 36
221071SERSERGLNGLN(chain 'r' and (resid 2 through 26 or resid 30...rHA30 - 12841 - 139
221081PROPROPHEPHE(chain 'r' and (resid 2 through 26 or resid 30...rHA132 - 258143 - 269
221091PHEPHELYSLYS(chain 'r' and (resid 2 through 26 or resid 30...rHA265 - 288276 - 299
221101PHEPHEVALVAL(chain 'r' and (resid 2 through 26 or resid 30...rHA292 - 323303 - 334
231111SERSERLYSLYS(chain 's' and (resid 2 through 26 or resid 30...sIA2 - 2513 - 36
231121SERSERGLNGLN(chain 's' and (resid 2 through 26 or resid 30...sIA30 - 12841 - 139
231131PROPROPHEPHE(chain 's' and (resid 2 through 26 or resid 30...sIA132 - 258143 - 269
231141PHEPHELYSLYS(chain 's' and (resid 2 through 26 or resid 30...sIA265 - 288276 - 299
231151PHEPHEVALVAL(chain 's' and (resid 2 through 26 or resid 30...sIA292 - 323303 - 334
241161SERSERLYSLYS(chain 't' and (resid 2 through 26 or resid 30...tJA2 - 2513 - 36
241171SERSERGLNGLN(chain 't' and (resid 2 through 26 or resid 30...tJA30 - 12841 - 139
241181PROPROPHEPHE(chain 't' and (resid 2 through 26 or resid 30...tJA132 - 258143 - 269
241191PHEPHELYSLYS(chain 't' and (resid 2 through 26 or resid 30...tJA265 - 288276 - 299
241201PHEPHEVALVAL(chain 't' and (resid 2 through 26 or resid 30...tJA292 - 323303 - 334
11212LEULEUILEILE(chain 'E' and resid 2 through 93)ESA2 - 9213 - 103
21222LEULEUILEILE(chain 'F' and resid 2 through 93)FTA2 - 9213 - 103
31232LEULEUILEILE(chain 'M' and resid 2 through 93)ME2 - 9213 - 103
41242LEULEUILEILE(chain 'N' and resid 2 through 93)NF2 - 9213 - 103
51252LEULEUILEILE(chain 'U' and resid 2 through 93)UM2 - 9213 - 103
61262LEULEUILEILE(chain 'V' and resid 2 through 93)VN2 - 9213 - 103
71272LEULEUILEILE(chain 'e' and resid 2 through 93)eU2 - 9213 - 103
81282LEULEUILEILE(chain 'f' and resid 2 through 93)fV2 - 9213 - 103
91292LEULEUILEILE(chain 'm' and resid 2 through 93)mCA2 - 9213 - 103
101302LEULEUILEILE(chain 'n' and resid 2 through 93)nDA2 - 9213 - 103
111312LEULEUILEILE(chain 'u' and resid 2 through 93)uKA2 - 9213 - 103
121322LEULEUILEILE(chain 'v' and resid 2 through 93)vLA2 - 9213 - 103
11333DTDTDCDC(chain 'G' and (resid 6 through 28 or resid 31 through 33))GUA6 - 286 - 28
11343DGDGDTDT(chain 'G' and (resid 6 through 28 or resid 31 through 33))GUA31 - 3331 - 33
21353DTDTDCDC(chain 'O' and (resid 6 through 28 or resid 31 through 33))OG6 - 286 - 28
21363DGDGDTDT(chain 'O' and (resid 6 through 28 or resid 31 through 33))OG31 - 3331 - 33
31373DTDTDCDC(chain 'W' and (resid 6 through 28 or resid 31 through 33))WO6 - 286 - 28
31383DGDGDTDT(chain 'W' and (resid 6 through 28 or resid 31 through 33))WO31 - 3331 - 33
41393DTDTDCDC(chain 'g' and (resid 6 through 28 or resid 31 through 33))gW6 - 286 - 28
41403DGDGDTDT(chain 'g' and (resid 6 through 28 or resid 31 through 33))gW31 - 3331 - 33
51413DTDTDCDC(chain 'o' and (resid 6 through 28 or resid 31 through 33))oEA6 - 286 - 28
51423DGDGDTDT(chain 'o' and (resid 6 through 28 or resid 31 through 33))oEA31 - 3331 - 33
61433DTDTDCDC(chain 'w' and (resid 6 through 28 or resid 31 through 33))wMA6 - 286 - 28
61443DGDGDTDT(chain 'w' and (resid 6 through 28 or resid 31 through 33))wMA31 - 3331 - 33
11454DTDTDCDC(chain 'H' and (resid 8 through 29 or resid 32 through 34))HVA8 - 298 - 29
11464DTDTDTDT(chain 'H' and (resid 8 through 29 or resid 32 through 34))HVA32 - 3432 - 34
21474DTDTDCDC(chain 'P' and (resid 8 through 29 or resid 32 through 34))PH8 - 298 - 29
21484DTDTDTDT(chain 'P' and (resid 8 through 29 or resid 32 through 34))PH32 - 3432 - 34
31494DTDTDCDC(chain 'X' and (resid 8 through 29 or resid 32 through 34))XP8 - 298 - 29
31504DTDTDTDT(chain 'X' and (resid 8 through 29 or resid 32 through 34))XP32 - 3432 - 34
41514DTDTDCDC(chain 'h' and (resid 8 through 29 or resid 32 through 34))hX8 - 298 - 29
41524DTDTDTDT(chain 'h' and (resid 8 through 29 or resid 32 through 34))hX32 - 3432 - 34
51534DTDTDCDC(chain 'p' and (resid 8 through 29 or resid 32 through 34))pFA8 - 298 - 29
51544DTDTDTDT(chain 'p' and (resid 8 through 29 or resid 32 through 34))pFA32 - 3432 - 34
61554DTDTDCDC(chain 'x' and (resid 8 through 29 or resid 32 through 34))xNA8 - 298 - 29
61564DTDTDTDT(chain 'x' and (resid 8 through 29 or resid 32 through 34))xNA32 - 3432 - 34

NCSアンサンブル:
ID
1
2
3
4

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要素

#1: タンパク質 ...
CRISPR-associated endonuclease Cas1


分子量: 37811.238 Da / 分子数: 24 / 由来タイプ: 組換発現
由来: (組換発現) Synechocystis sp. (strain PCC 6803 / Kazusa) (バクテリア)
株: PCC 6803 / Kazusa / 遺伝子: cas1, slr7016 / 発現宿主: Escherichia coli (大腸菌)
参照: UniProt: Q6ZEI2, 加水分解酵素; エステル加水分解酵素
#2: タンパク質
CRISPR-associated endoribonuclease Cas2 1


分子量: 11656.425 Da / 分子数: 12 / 由来タイプ: 組換発現
由来: (組換発現) Synechocystis sp. (strain PCC 6803 / Kazusa) (バクテリア)
株: PCC 6803 / Kazusa / 遺伝子: cas2-1, ssr7017 / 発現宿主: Escherichia coli (大腸菌)
参照: UniProt: Q6ZEI1, 加水分解酵素; エステル加水分解酵素
#3: DNA鎖
DNA (36-MER)


分子量: 11004.026 Da / 分子数: 6 / 由来タイプ: 合成 / 由来: (合成) synthetic construct (人工物)
#4: DNA鎖
DNA (36-MER)


分子量: 11058.110 Da / 分子数: 6 / 由来タイプ: 合成 / 由来: (合成) synthetic construct (人工物)

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実験情報

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実験

実験手法: X線回折 / 使用した結晶の数: 1

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試料調製

結晶マシュー密度: 3.18 Å3/Da / 溶媒含有率: 61.34 %
結晶化温度: 293 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 6.5
詳細: 30% MPD, 0.1 M imidazole pH 6.5, 0.2 M (NH4)2SO4, 10% (w/v) PEG 3350

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データ収集

回折平均測定温度: 100 K / Serial crystal experiment: N
放射光源由来: シンクロトロン / サイト: SSRF / ビームライン: BL19U1 / 波長: 0.979 Å
検出器タイプ: DECTRIS PILATUS3 6M / 検出器: PIXEL / 日付: 2018年9月26日
放射プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長波長: 0.979 Å / 相対比: 1
反射解像度: 3.69→50 Å / Num. obs: 157305 / % possible obs: 99.9 % / 冗長度: 10.5 % / Biso Wilson estimate: 130.45 Å2 / CC1/2: 0.998 / Net I/σ(I): 12.68
反射 シェル解像度: 3.69→3.92 Å / Num. unique obs: 25305 / CC1/2: 0.838

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解析

ソフトウェア
名称バージョン分類
PHENIX1.15.2_3472精密化
PDB_EXTRACT3.25データ抽出
XDSデータ削減
XDSデータスケーリング
PHASER位相決定
精密化構造決定の手法: 分子置換
開始モデル: 7CR6

7cr6


解像度: 3.7→47.56 Å / SU ML: 0.7752 / 交差検証法: THROUGHOUT / σ(F): 1.93 / 位相誤差: 42.3464
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.3409 1566 1 %
Rwork0.2955 155399 -
obs0.2959 156965 99.78 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL
原子変位パラメータBiso mean: 147.92 Å2
精密化ステップサイクル: LAST / 解像度: 3.7→47.56 Å
タンパク質核酸リガンド溶媒全体
原子数71378 7242 0 0 78620
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.004181050
X-RAY DIFFRACTIONf_angle_d0.9485111106
X-RAY DIFFRACTIONf_chiral_restr0.043412313
X-RAY DIFFRACTIONf_plane_restr0.005913021
X-RAY DIFFRACTIONf_dihedral_angle_d10.865947316
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.7-3.820.46921420.394914089X-RAY DIFFRACTION99.65
3.82-3.950.49261430.375414153X-RAY DIFFRACTION99.71
3.95-4.110.36861420.348714093X-RAY DIFFRACTION99.84
4.11-4.30.36151420.340414211X-RAY DIFFRACTION99.89
4.3-4.520.36121430.310414156X-RAY DIFFRACTION99.88
4.52-4.810.331410.296414064X-RAY DIFFRACTION99.96
4.81-5.180.36461440.30714187X-RAY DIFFRACTION99.92
5.18-5.70.40891420.320514118X-RAY DIFFRACTION99.99
5.7-6.520.34821430.33214150X-RAY DIFFRACTION99.97
6.52-8.210.37541430.296314173X-RAY DIFFRACTION99.94
8.21-47.560.23011410.214714005X-RAY DIFFRACTION98.85

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万見について

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お知らせ

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2022年2月9日: EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

  • EMDBのヘッダファイルのバージョン3が、公式のフォーマットとなりました。
  • これまでは公式だったバージョン1.9は、アーカイブから削除されます。

関連情報:EMDBヘッダ

外部リンク:wwPDBはEMDBデータモデルのバージョン3へ移行します

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2020年8月12日: 新型コロナ情報

新型コロナ情報

URL: https://pdbj.org/emnavi/covid19.php

新ページ: EM Navigatorに新型コロナウイルスの特設ページを開設しました。

関連情報:Covid-19情報 / 2020年3月5日: 新型コロナウイルスの構造データ

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2020年3月5日: 新型コロナウイルスの構造データ

新型コロナウイルスの構造データ

関連情報:万見生物種 / 2020年8月12日: 新型コロナ情報

外部リンク:COVID-19特集ページ - PDBj / 今月の分子2020年2月：コロナウイルスプロテーアーゼ

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2019年1月31日: EMDBのIDの桁数の変更

EMDBのIDの桁数の変更

  • EMDBエントリに付与されているアクセスコード(EMDB-ID)は4桁の数字(例、EMD-1234)でしたが、間もなく枯渇します。これまでの4桁のID番号は4桁のまま変更されませんが、4桁の数字を使い切った後に発行されるIDは5桁以上の数字(例、EMD-12345)になります。5桁のIDは2019年の春頃から発行される見通しです。
  • EM Navigator/万見では、接頭語「EMD-」は省略されています。

関連情報:Q: 「EMD」とは何ですか？ / 万見/EM NavigatorにおけるID/アクセスコードの表記

外部リンク:EMDB Accession Codes are Changing Soon! / PDBjへお問い合わせ

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2017年7月12日: PDB大規模アップデート

PDB大規模アップデート

  • 新バージョンのPDBx/mmCIF辞書形式に基づくデータがリリースされました。
  • 今回の更新はバージョン番号が4から5になる大規模なもので、全エントリデータの書き換えが行われる「Remediation」というアップデートに該当します。
  • このバージョンアップで、電子顕微鏡の実験手法に関する多くの項目の書式が改定されました(例：em_softwareなど)。
  • EM NavigatorとYorodumiでも、この改定に基づいた表示内容になります。

外部リンク:wwPDB Remediation / OneDepデータ基準に準拠した、より強化された内容のモデル構造ファイルが、PDBアーカイブで公開されました。

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万見 (Yorodumi)

幾万の構造データを、幾万の視点から

  • 万見(Yorodumi)は、EMDB/PDB/SASBDBなどの構造データを閲覧するためのページです。
  • EM Navigatorの詳細ページの後継、Omokage検索のフロントエンドも兼ねています。

関連情報:EMDB / PDB / SASBDB / 3つのデータバンクの比較 / 万見検索 / 2016年8月31日: 新しいEM Navigatorと万見 / 万見文献 / Jmol/JSmol / 機能・相同性情報 / 新しいEM Navigatorと万見の変更点

他の情報も見る